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consider making customized allocations for mosdepth

Status: Open.

#93 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Feb 6, 2025

Add coverage and insert size plots

Status: Open.

#91 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Jan 10, 2025

expand possible number of mosdepth quantize bins

Status: Open.

#87 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Oct 30, 2024

update method of specifying which algorithms to run

Status: Open.

#85 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Oct 29, 2024

update picard to 3.3.0

Status: Open.

#81 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Oct 17, 2024

update samtools to v1.21

Status: Open.

#80 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Oct 17, 2024

add checksums generation

Status: Open.

#78 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Aug 19, 2024

Use store_object_as_json to store parameters

standardizationStandardization taskStandardization task

Status: Open.

#77 In uclahs-cds/pipeline-generate-SQC-BAM;

· nwiltsie opened on Aug 12, 2024

Add checksum generation

Status: Open.

#76 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Jul 30, 2024

For some processes (FastQC, SAMtools stats), set cpu allocation to 1 if the number of readgroups is large. Do this within methods.config

Status: Open.

#69 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Jun 20, 2024

optimize for usage in metapipeline

Status: Open.

#68 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Jun 20, 2024

Max number of individual readgroups for samtools stats

Status: Open.

#66 In uclahs-cds/pipeline-generate-SQC-BAM;

· sorelfitzgibbon opened on Jun 20, 2024